Just experienced this problem on 4.1.2... not easy to workaround when all you have is an .ova file.

I looked at the trunk svn for vboxmanage and could find no evidence of change there of the sort I would expect -- which is "import" commands to ignore shared folder specs (as for e.g. a floppy) and dry-run check that the shared folder is ok.

I agree that, from the GUI, it would be nice to have a prompt for the updated folders.

My variant of the problem was exporting a Debian VM from Win7 and importing on an Ubuntu machine. I'd just updated the Ubuntu vb to 4.1.2 (why is "natty" still 4.0.4). My workaround was to use "sed" on the .ova file to edit the bad path to one in /tmp that had the same number of characters.